Starting phenix.real_space_refine on Sat Jul 4 16:08:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9t_64887/07_2026/9v9t_64887.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9t_64887/07_2026/9v9t_64887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9t_64887/07_2026/9v9t_64887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9t_64887/07_2026/9v9t_64887.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9t_64887/07_2026/9v9t_64887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9t_64887/07_2026/9v9t_64887.cif" } resolution = 2.9 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11108 atoms to isotropic. 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 263 5.49 5 S 28 5.16 5 C 7422 2.51 5 N 2452 2.21 5 O 2970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 13137 Number of models: 1 Model: "" Number of chains: 16 Chain: "L" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 362 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "N" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 252 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 815 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 711 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "K" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "I" Number of atoms: 2671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2671 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "J" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2721 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 39 SG CYS L 27 78.197 34.269 53.057 1.00 53.67 S ATOM 58 SG CYS L 30 76.326 32.534 50.130 1.00 53.74 S ATOM 146 SG CYS L 41 79.766 34.517 49.916 1.00 54.84 S ATOM 166 SG CYS L 44 76.560 36.219 49.956 1.00 56.02 S ATOM 401 SG CYS N 27 42.491 93.859 43.107 1.00 65.60 S ATOM 420 SG CYS N 30 41.687 93.175 39.591 1.00 69.15 S ATOM 508 SG CYS N 41 38.896 92.922 42.019 1.00 67.02 S ATOM 528 SG CYS N 44 41.615 90.268 42.201 1.00 67.95 S Time building chain proxies: 3.09, per 1000 atoms: 0.24 Number of scatterers: 13137 At special positions: 0 Unit cell: (123.2, 122.1, 117.7, 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 28 16.00 P 263 15.00 O 2970 8.00 N 2452 7.00 C 7422 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 404.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 41 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 44 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 30 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 27 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 30 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 27 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 41 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 44 " Number of angles added : 12 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 15 sheets defined 59.6% alpha, 3.9% beta 129 base pairs and 220 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'L' and resid 59 through 67 removed outlier: 3.632A pdb=" N ALA L 63 " --> pdb=" O SER L 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.193A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.731A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.928A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.547A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.666A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 4.063A pdb=" N SER D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.941A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA D 121 " --> pdb=" O CYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.567A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.590A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.764A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.581A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.586A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.567A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.835A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 34 Processing helix chain 'K' and resid 55 through 59 Processing helix chain 'O' and resid 22 through 34 Processing helix chain 'O' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'N' and resid 25 through 26 removed outlier: 3.545A pdb=" N TRP N 25 " --> pdb=" O ASN N 34 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASN N 34 " --> pdb=" O TRP N 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.021A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.942A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA8, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.088A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.222A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'K' and resid 48 through 49 removed outlier: 4.026A pdb=" N PHE K 45 " --> pdb=" O LYS K 48 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG K 42 " --> pdb=" O VAL K 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 3 through 4 removed outlier: 3.598A pdb=" N PHE O 4 " --> pdb=" O SER O 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'O' and resid 44 through 45 removed outlier: 3.793A pdb=" N PHE O 45 " --> pdb=" O LYS O 48 " (cutoff:3.500A) 421 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 333 hydrogen bonds 662 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 220 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.49 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: 3290 1.34 - 1.46: 4009 1.46 - 1.58: 6029 1.58 - 1.70: 524 1.70 - 1.82: 40 Bond restraints: 13892 Sorted by residual: bond pdb=" C1' DC I 3 " pdb=" N1 DC I 3 " ideal model delta sigma weight residual 1.468 1.532 -0.064 1.40e-02 5.10e+03 2.08e+01 bond pdb=" C3' DC J 115 " pdb=" C2' DC J 115 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DG J 136 " pdb=" C2' DG J 136 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.25e+01 bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC I 118 " pdb=" C2' DC I 118 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 ... (remaining 13887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 19415 2.23 - 4.46: 451 4.46 - 6.69: 11 6.69 - 8.91: 0 8.91 - 11.14: 2 Bond angle restraints: 19879 Sorted by residual: angle pdb=" N3 DT J 35 " pdb=" C4 DT J 35 " pdb=" O4 DT J 35 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 112 " pdb=" C4 DT I 112 " pdb=" O4 DT I 112 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT J 24 " pdb=" C4 DT J 24 " pdb=" O4 DT J 24 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 19874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 6463 35.89 - 71.78: 1225 71.78 - 107.67: 18 107.67 - 143.56: 1 143.56 - 179.45: 3 Dihedral angle restraints: 7710 sinusoidal: 4876 harmonic: 2834 Sorted by residual: dihedral pdb=" C4' DC I 3 " pdb=" C3' DC I 3 " pdb=" O3' DC I 3 " pdb=" P DG I 4 " ideal model delta sinusoidal sigma weight residual 220.00 40.55 179.45 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 57 " pdb=" C3' DT J 57 " pdb=" O3' DT J 57 " pdb=" P DT J 58 " ideal model delta sinusoidal sigma weight residual -140.00 35.95 -175.95 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 70.27 149.73 1 3.50e+01 8.16e-04 1.46e+01 ... (remaining 7707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1223 0.030 - 0.060: 687 0.060 - 0.090: 248 0.090 - 0.119: 102 0.119 - 0.149: 16 Chirality restraints: 2276 Sorted by residual: chirality pdb=" CA ILE O 3 " pdb=" N ILE O 3 " pdb=" C ILE O 3 " pdb=" CB ILE O 3 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" C3' DT J 57 " pdb=" C4' DT J 57 " pdb=" O3' DT J 57 " pdb=" C2' DT J 57 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" C3' DG I 4 " pdb=" C4' DG I 4 " pdb=" O3' DG I 4 " pdb=" C2' DG I 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2273 not shown) Planarity restraints: 1607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " -0.024 2.00e-02 2.50e+03 1.07e-02 3.18e+00 pdb=" N9 DA I 20 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO G 80 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 39 " 0.024 2.00e-02 2.50e+03 1.05e-02 3.01e+00 pdb=" N9 DA I 39 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 39 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 39 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 39 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 39 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 39 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 39 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 39 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 39 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 39 " -0.001 2.00e-02 2.50e+03 ... (remaining 1604 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 206 2.65 - 3.21: 10613 3.21 - 3.77: 22377 3.77 - 4.34: 30972 4.34 - 4.90: 44570 Nonbonded interactions: 108738 Sorted by model distance: nonbonded pdb=" O2 DC I 95 " pdb=" N2 DG J 53 " model vdw 2.085 2.496 nonbonded pdb=" OG1 THR L 50 " pdb=" OE1 GLU G 64 " model vdw 2.206 3.040 nonbonded pdb=" NE2 GLN K 31 " pdb=" O ILE K 36 " model vdw 2.271 3.120 nonbonded pdb=" OE1 GLN K 62 " pdb=" OG SER K 65 " model vdw 2.294 3.040 nonbonded pdb=" NH2 ARG L 53 " pdb=" OD2 ASP G 90 " model vdw 2.310 3.120 ... (remaining 108733 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 39 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 22 through 100) selection = (chain 'F' and resid 22 through 100) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 119) } ncs_group { reference = (chain 'D' and resid 30 through 120) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.850 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 0.067 13900 Z= 0.488 Angle : 0.760 11.143 19891 Z= 0.638 Chirality : 0.044 0.149 2276 Planarity : 0.004 0.044 1607 Dihedral : 26.332 179.447 5872 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.27), residues: 952 helix: 1.76 (0.22), residues: 555 sheet: -0.89 (0.94), residues: 32 loop : -1.67 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.015 0.002 TYR F 88 PHE 0.011 0.001 PHE E 84 TRP 0.004 0.001 TRP N 25 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.49 (13892) covalent geometry : angle 0.74578 / 0.64 (19879) hydrogen bonds : bond 0.12422 / 8.07 ( 754) hydrogen bonds : angle 4.16582 / 3.02 ( 1892) metal coordination : bond 0.00718 / 0.36 ( 8) metal coordination : angle 5.98401 / 3.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.376 Fit side-chains REVERT: A 77 ASP cc_start: 0.6292 (m-30) cc_final: 0.6069 (m-30) REVERT: C 94 ASN cc_start: 0.8857 (t0) cc_final: 0.8608 (t0) REVERT: D 32 GLU cc_start: 0.6790 (pt0) cc_final: 0.6520 (pt0) REVERT: D 113 LYS cc_start: 0.7856 (tttm) cc_final: 0.7627 (tttp) REVERT: G 73 ASN cc_start: 0.7561 (t0) cc_final: 0.7109 (t0) REVERT: G 74 LYS cc_start: 0.7393 (mmtm) cc_final: 0.7174 (tppt) REVERT: H 102 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6565 (tp30) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.9372 time to fit residues: 148.7233 Evaluate side-chains 135 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 125 GLN C 110 ASN E 76 GLN E 125 GLN G 84 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.173667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.127400 restraints weight = 14341.294| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.08 r_work: 0.3044 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 13900 Z= 0.278 Angle : 0.835 19.815 19891 Z= 0.457 Chirality : 0.057 0.264 2276 Planarity : 0.007 0.053 1607 Dihedral : 30.214 178.076 3934 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.56 % Allowed : 11.04 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.26), residues: 952 helix: 1.16 (0.21), residues: 568 sheet: -0.97 (1.06), residues: 27 loop : -2.05 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 36 TYR 0.018 0.003 TYR A 54 PHE 0.019 0.003 PHE E 84 TRP 0.013 0.003 TRP N 25 HIS 0.005 0.002 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.28 (13892) covalent geometry : angle 0.81446 / 0.46 (19879) hydrogen bonds : bond 0.08648 / 5.72 ( 754) hydrogen bonds : angle 3.57431 / 2.62 ( 1892) metal coordination : bond 0.01197 / 0.62 ( 8) metal coordination : angle 7.54273 / 4.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.438 Fit side-chains REVERT: A 77 ASP cc_start: 0.7321 (m-30) cc_final: 0.7092 (m-30) REVERT: D 32 GLU cc_start: 0.7044 (pt0) cc_final: 0.6618 (pt0) REVERT: D 56 MET cc_start: 0.8665 (mmt) cc_final: 0.8401 (tpt) REVERT: D 113 LYS cc_start: 0.8301 (tttm) cc_final: 0.7992 (tttp) REVERT: E 50 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8008 (mm-30) REVERT: G 73 ASN cc_start: 0.7815 (t0) cc_final: 0.7196 (t0) REVERT: G 84 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.7482 (tm130) REVERT: K 1 MET cc_start: 0.3143 (OUTLIER) cc_final: 0.2848 (ptt) outliers start: 13 outliers final: 2 residues processed: 139 average time/residue: 0.9115 time to fit residues: 134.1789 Evaluate side-chains 135 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain K residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 102 optimal weight: 30.0000 chunk 39 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 chunk 117 optimal weight: 30.0000 chunk 58 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 125 GLN C 110 ASN E 76 GLN E 125 GLN G 84 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.177478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133000 restraints weight = 14634.664| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.05 r_work: 0.3122 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13900 Z= 0.144 Angle : 0.657 13.361 19891 Z= 0.374 Chirality : 0.047 0.247 2276 Planarity : 0.005 0.060 1607 Dihedral : 30.165 175.708 3934 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.56 % Allowed : 12.73 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.81 (0.27), residues: 952 helix: 1.96 (0.22), residues: 565 sheet: -1.14 (0.92), residues: 34 loop : -1.74 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 20 TYR 0.010 0.001 TYR K 59 PHE 0.008 0.001 PHE A 67 TRP 0.006 0.001 TRP N 25 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (13892) covalent geometry : angle 0.64241 / 0.37 (19879) hydrogen bonds : bond 0.06087 / 4.03 ( 754) hydrogen bonds : angle 3.22119 / 2.36 ( 1892) metal coordination : bond 0.00735 / 0.41 ( 8) metal coordination : angle 5.70510 / 3.47 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.484 Fit side-chains REVERT: A 77 ASP cc_start: 0.7221 (m-30) cc_final: 0.6994 (m-30) REVERT: D 32 GLU cc_start: 0.6935 (pt0) cc_final: 0.6552 (pt0) REVERT: D 113 LYS cc_start: 0.8282 (tttm) cc_final: 0.7979 (tttp) REVERT: E 50 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7950 (mm-30) REVERT: G 73 ASN cc_start: 0.7785 (t0) cc_final: 0.7147 (t0) REVERT: G 91 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: H 105 LYS cc_start: 0.8369 (tttm) cc_final: 0.8137 (tttm) outliers start: 13 outliers final: 5 residues processed: 140 average time/residue: 0.8877 time to fit residues: 131.9349 Evaluate side-chains 136 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 110 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 36 optimal weight: 0.6980 chunk 114 optimal weight: 20.0000 chunk 88 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 125 GLN C 110 ASN E 76 GLN E 125 GLN K 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.175881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.128335 restraints weight = 14393.540| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.12 r_work: 0.3120 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13900 Z= 0.174 Angle : 0.686 17.500 19891 Z= 0.384 Chirality : 0.049 0.240 2276 Planarity : 0.005 0.042 1607 Dihedral : 30.161 176.925 3934 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.40 % Allowed : 13.69 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.27), residues: 952 helix: 1.95 (0.21), residues: 565 sheet: -1.18 (0.92), residues: 34 loop : -1.75 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 77 TYR 0.011 0.002 TYR F 51 PHE 0.015 0.002 PHE E 84 TRP 0.010 0.002 TRP N 25 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (13892) covalent geometry : angle 0.66808 / 0.38 (19879) hydrogen bonds : bond 0.06645 / 4.41 ( 754) hydrogen bonds : angle 3.21041 / 2.34 ( 1892) metal coordination : bond 0.00878 / 0.47 ( 8) metal coordination : angle 6.31243 / 3.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.373 Fit side-chains REVERT: A 77 ASP cc_start: 0.7179 (m-30) cc_final: 0.6933 (m-30) REVERT: D 32 GLU cc_start: 0.6669 (pt0) cc_final: 0.6357 (pt0) REVERT: D 90 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: D 113 LYS cc_start: 0.8265 (tttm) cc_final: 0.7924 (tttp) REVERT: E 50 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7793 (mm-30) REVERT: G 73 ASN cc_start: 0.7765 (t0) cc_final: 0.7074 (t0) REVERT: G 91 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7293 (tt0) REVERT: H 105 LYS cc_start: 0.8330 (tttm) cc_final: 0.8111 (tttm) REVERT: K 24 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6249 (tm-30) outliers start: 20 outliers final: 7 residues processed: 136 average time/residue: 0.9304 time to fit residues: 134.0117 Evaluate side-chains 138 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 24 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 107 optimal weight: 40.0000 chunk 99 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 125 GLN C 110 ASN E 76 GLN E 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.173728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.126308 restraints weight = 14429.901| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.18 r_work: 0.3087 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13900 Z= 0.251 Angle : 0.792 17.514 19891 Z= 0.433 Chirality : 0.055 0.263 2276 Planarity : 0.006 0.046 1607 Dihedral : 30.342 178.183 3934 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.64 % Allowed : 15.49 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.20 (0.27), residues: 952 helix: 1.46 (0.21), residues: 567 sheet: -1.30 (0.93), residues: 34 loop : -2.01 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 53 TYR 0.016 0.003 TYR A 54 PHE 0.021 0.002 PHE E 84 TRP 0.016 0.003 TRP N 25 HIS 0.006 0.002 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 (13892) covalent geometry : angle 0.77665 / 0.43 (19879) hydrogen bonds : bond 0.08177 / 5.43 ( 754) hydrogen bonds : angle 3.38222 / 2.46 ( 1892) metal coordination : bond 0.01203 / 0.63 ( 8) metal coordination : angle 6.35337 / 3.76 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.364 Fit side-chains REVERT: A 59 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7297 (pm20) REVERT: A 77 ASP cc_start: 0.7201 (m-30) cc_final: 0.6967 (m-30) REVERT: D 32 GLU cc_start: 0.6840 (pt0) cc_final: 0.6517 (pt0) REVERT: D 68 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7620 (mt-10) REVERT: D 90 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: D 113 LYS cc_start: 0.8302 (tttm) cc_final: 0.8037 (tttp) REVERT: E 50 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7805 (mm-30) REVERT: G 73 ASN cc_start: 0.7823 (t0) cc_final: 0.7170 (t0) REVERT: G 91 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7404 (tm-30) REVERT: K 24 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6279 (tm-30) outliers start: 22 outliers final: 9 residues processed: 144 average time/residue: 0.8541 time to fit residues: 130.1280 Evaluate side-chains 143 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain O residue 57 SER Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 16 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 117 optimal weight: 30.0000 chunk 64 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN L 64 GLN A 125 GLN C 110 ASN D 60 ASN E 76 GLN E 125 GLN K 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.179047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.138453 restraints weight = 13999.838| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 0.99 r_work: 0.3216 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.003 0.036 13900 Z= 0.156 Angle : 0.691 17.580 19891 Z= 0.382 Chirality : 0.049 0.241 2276 Planarity : 0.004 0.046 1607 Dihedral : 30.297 176.331 3934 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.16 % Allowed : 17.17 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.27), residues: 952 helix: 1.96 (0.21), residues: 564 sheet: -1.19 (0.96), residues: 34 loop : -1.80 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 77 TYR 0.010 0.002 TYR F 88 PHE 0.010 0.001 PHE E 84 TRP 0.010 0.002 TRP N 25 HIS 0.003 0.001 HIS O 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (13892) covalent geometry : angle 0.66689 / 0.38 (19879) hydrogen bonds : bond 0.06452 / 4.28 ( 754) hydrogen bonds : angle 3.16713 / 2.30 ( 1892) metal coordination : bond 0.01114 / 0.58 ( 8) metal coordination : angle 7.36702 / 4.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.380 Fit side-chains REVERT: A 59 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7328 (pm20) REVERT: D 32 GLU cc_start: 0.6732 (pt0) cc_final: 0.6468 (pt0) REVERT: D 68 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7780 (mt-10) REVERT: D 90 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: D 113 LYS cc_start: 0.8268 (tttm) cc_final: 0.7989 (tttp) REVERT: E 50 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7963 (mm-30) REVERT: F 74 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: G 73 ASN cc_start: 0.7872 (t0) cc_final: 0.7213 (t0) REVERT: G 91 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7579 (tm-30) REVERT: K 24 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6242 (tm-30) outliers start: 18 outliers final: 9 residues processed: 138 average time/residue: 0.8999 time to fit residues: 131.6490 Evaluate side-chains 141 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain O residue 57 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 107 optimal weight: 40.0000 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 68 GLN A 125 GLN C 110 ASN E 76 GLN E 125 GLN K 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.177583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136632 restraints weight = 13938.149| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 0.99 r_work: 0.3190 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13900 Z= 0.211 Angle : 0.745 18.034 19891 Z= 0.408 Chirality : 0.052 0.258 2276 Planarity : 0.005 0.055 1607 Dihedral : 30.327 177.653 3934 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.76 % Allowed : 17.29 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.27), residues: 952 helix: 1.72 (0.21), residues: 567 sheet: -1.26 (0.97), residues: 34 loop : -1.93 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 77 TYR 0.013 0.002 TYR F 51 PHE 0.018 0.002 PHE E 84 TRP 0.013 0.002 TRP N 25 HIS 0.005 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (13892) covalent geometry : angle 0.72347 / 0.41 (19879) hydrogen bonds : bond 0.07371 / 4.89 ( 754) hydrogen bonds : angle 3.24510 / 2.35 ( 1892) metal coordination : bond 0.01024 / 0.55 ( 8) metal coordination : angle 7.24935 / 4.35 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.380 Fit side-chains REVERT: A 59 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7349 (pm20) REVERT: D 32 GLU cc_start: 0.6932 (pt0) cc_final: 0.6615 (pt0) REVERT: D 90 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: D 113 LYS cc_start: 0.8283 (tttm) cc_final: 0.8018 (tttp) REVERT: E 50 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7990 (mm-30) REVERT: G 73 ASN cc_start: 0.7768 (t0) cc_final: 0.7061 (t0) REVERT: G 91 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: K 24 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6255 (tm-30) outliers start: 23 outliers final: 10 residues processed: 137 average time/residue: 0.8383 time to fit residues: 121.8210 Evaluate side-chains 141 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain O residue 57 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 95 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 125 GLN C 110 ASN E 76 GLN E 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.177674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136017 restraints weight = 13874.818| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.00 r_work: 0.3193 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13900 Z= 0.205 Angle : 0.743 17.555 19891 Z= 0.406 Chirality : 0.052 0.263 2276 Planarity : 0.005 0.056 1607 Dihedral : 30.355 177.165 3934 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.00 % Allowed : 17.65 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.27), residues: 952 helix: 1.71 (0.21), residues: 566 sheet: -1.32 (0.98), residues: 34 loop : -1.88 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 53 TYR 0.013 0.002 TYR H 34 PHE 0.016 0.002 PHE E 84 TRP 0.013 0.002 TRP N 25 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.20 (13892) covalent geometry : angle 0.72183 / 0.40 (19879) hydrogen bonds : bond 0.07206 / 4.78 ( 754) hydrogen bonds : angle 3.22963 / 2.34 ( 1892) metal coordination : bond 0.00951 / 0.51 ( 8) metal coordination : angle 7.14268 / 4.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.367 Fit side-chains REVERT: A 59 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: D 32 GLU cc_start: 0.6739 (pt0) cc_final: 0.6441 (pt0) REVERT: D 68 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7842 (mt-10) REVERT: D 90 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: D 113 LYS cc_start: 0.8276 (tttm) cc_final: 0.8012 (tttp) REVERT: E 50 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7993 (mm-30) REVERT: E 56 LYS cc_start: 0.8627 (tppp) cc_final: 0.8402 (tttt) REVERT: F 59 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8403 (ttpm) REVERT: G 73 ASN cc_start: 0.7788 (t0) cc_final: 0.7124 (t0) REVERT: G 91 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: K 24 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6232 (tm-30) outliers start: 25 outliers final: 12 residues processed: 141 average time/residue: 0.8226 time to fit residues: 123.0802 Evaluate side-chains 145 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain O residue 57 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 56 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 116 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 105 optimal weight: 50.0000 chunk 98 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 125 GLN C 110 ASN E 76 GLN E 125 GLN K 31 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.180556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140134 restraints weight = 14123.922| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 0.99 r_work: 0.3238 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13900 Z= 0.135 Angle : 0.664 14.793 19891 Z= 0.371 Chirality : 0.047 0.231 2276 Planarity : 0.004 0.044 1607 Dihedral : 30.265 176.050 3934 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.28 % Allowed : 18.49 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.07 (0.28), residues: 952 helix: 2.22 (0.22), residues: 564 sheet: -1.29 (0.99), residues: 34 loop : -1.71 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 77 TYR 0.013 0.001 TYR F 51 PHE 0.009 0.001 PHE L 39 TRP 0.008 0.001 TRP N 25 HIS 0.002 0.001 HIS O 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.13 (13892) covalent geometry : angle 0.64534 / 0.37 (19879) hydrogen bonds : bond 0.05825 / 3.87 ( 754) hydrogen bonds : angle 3.06290 / 2.22 ( 1892) metal coordination : bond 0.00634 / 0.36 ( 8) metal coordination : angle 6.33927 / 3.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.225 Fit side-chains REVERT: A 59 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7345 (pm20) REVERT: D 32 GLU cc_start: 0.6722 (pt0) cc_final: 0.6404 (pt0) REVERT: D 68 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7748 (mt-10) REVERT: D 113 LYS cc_start: 0.8246 (tttm) cc_final: 0.7987 (tttp) REVERT: E 50 GLU cc_start: 0.8229 (mm-30) cc_final: 0.8004 (mm-30) REVERT: E 56 LYS cc_start: 0.8649 (tppp) cc_final: 0.8407 (tttt) REVERT: F 59 LYS cc_start: 0.8697 (tptm) cc_final: 0.8402 (ttpm) REVERT: F 92 ARG cc_start: 0.8373 (ttp80) cc_final: 0.8153 (ttp80) REVERT: G 73 ASN cc_start: 0.7788 (t0) cc_final: 0.7190 (t0) REVERT: G 91 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7423 (tt0) REVERT: K 24 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6216 (tm-30) outliers start: 19 outliers final: 11 residues processed: 143 average time/residue: 0.8252 time to fit residues: 125.2538 Evaluate side-chains 141 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 3 optimal weight: 0.0470 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 105 optimal weight: 50.0000 chunk 7 optimal weight: 0.0170 chunk 5 optimal weight: 6.9990 chunk 117 optimal weight: 40.0000 chunk 59 optimal weight: 4.9990 overall best weight: 2.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 68 GLN A 125 GLN C 110 ASN E 76 GLN E 125 GLN K 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.179441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.138770 restraints weight = 14053.772| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 0.99 r_work: 0.3219 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13900 Z= 0.161 Angle : 0.685 20.652 19891 Z= 0.377 Chirality : 0.048 0.246 2276 Planarity : 0.005 0.057 1607 Dihedral : 30.232 176.756 3934 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.28 % Allowed : 18.97 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.28), residues: 952 helix: 2.11 (0.22), residues: 566 sheet: -2.23 (0.85), residues: 43 loop : -1.63 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 77 TYR 0.013 0.002 TYR F 88 PHE 0.012 0.002 PHE E 84 TRP 0.009 0.002 TRP N 25 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (13892) covalent geometry : angle 0.65926 / 0.38 (19879) hydrogen bonds : bond 0.06235 / 4.14 ( 754) hydrogen bonds : angle 3.08989 / 2.24 ( 1892) metal coordination : bond 0.00865 / 0.47 ( 8) metal coordination : angle 7.53933 / 4.51 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.278 Fit side-chains REVERT: A 59 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7382 (pm20) REVERT: D 32 GLU cc_start: 0.6755 (pt0) cc_final: 0.6439 (pt0) REVERT: D 68 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7721 (mt-10) REVERT: D 113 LYS cc_start: 0.8281 (tttm) cc_final: 0.8027 (tttp) REVERT: E 50 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8033 (mm-30) REVERT: E 56 LYS cc_start: 0.8612 (tppp) cc_final: 0.8334 (tttt) REVERT: F 59 LYS cc_start: 0.8746 (tptm) cc_final: 0.8401 (ttpm) REVERT: F 92 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8116 (ttp80) REVERT: G 73 ASN cc_start: 0.7768 (t0) cc_final: 0.7247 (t0) REVERT: G 91 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: K 24 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6180 (tm-30) outliers start: 19 outliers final: 13 residues processed: 141 average time/residue: 0.8150 time to fit residues: 121.8099 Evaluate side-chains 146 residues out of total 833 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain O residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 9 optimal weight: 7.9990 chunk 95 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 110 optimal weight: 20.0000 chunk 68 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 34 ASN A 68 GLN A 125 GLN C 110 ASN E 76 GLN E 125 GLN K 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.179541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.138372 restraints weight = 13956.780| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.00 r_work: 0.3208 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13900 Z= 0.158 Angle : 0.682 19.642 19891 Z= 0.376 Chirality : 0.048 0.246 2276 Planarity : 0.005 0.061 1607 Dihedral : 30.232 176.573 3934 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.52 % Allowed : 18.73 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.28), residues: 952 helix: 2.11 (0.22), residues: 566 sheet: -2.24 (0.85), residues: 43 loop : -1.62 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 77 TYR 0.012 0.002 TYR F 51 PHE 0.012 0.001 PHE E 84 TRP 0.009 0.002 TRP N 25 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (13892) covalent geometry : angle 0.65841 / 0.37 (19879) hydrogen bonds : bond 0.06192 / 4.11 ( 754) hydrogen bonds : angle 3.08619 / 2.24 ( 1892) metal coordination : bond 0.00875 / 0.47 ( 8) metal coordination : angle 7.25463 / 4.34 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4640.47 seconds wall clock time: 79 minutes 22.38 seconds (4762.38 seconds total)