Starting phenix.real_space_refine on Fri Aug 7 11:31:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v9s_64886/08_2026/9v9s_64886.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v9s_64886/08_2026/9v9s_64886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v9s_64886/08_2026/9v9s_64886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v9s_64886/08_2026/9v9s_64886.map" model { file = "/net/cci-nas-00/data/ceres_data/9v9s_64886/08_2026/9v9s_64886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v9s_64886/08_2026/9v9s_64886.cif" } resolution = 3.8 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= 0.003 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 10725 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 245 5.49 5 S 28 5.16 5 C 7234 2.51 5 N 2378 2.21 5 O 2861 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12748 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: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} 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: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 774 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 652 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} 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: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2485 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "J" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2538 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} 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 72.784 34.886 54.356 1.00 91.05 S ATOM 58 SG CYS L 30 72.537 32.573 51.376 1.00 95.53 S ATOM 146 SG CYS L 41 75.224 35.217 51.356 1.00 88.03 S ATOM 166 SG CYS L 44 71.638 36.332 51.086 1.00 87.51 S ATOM 401 SG CYS N 27 37.831 95.429 43.471 1.00104.89 S ATOM 420 SG CYS N 30 37.453 94.914 39.720 1.00106.82 S ATOM 508 SG CYS N 41 34.736 93.657 41.944 1.00102.49 S ATOM 528 SG CYS N 44 38.005 91.880 42.018 1.00 96.30 S Time building chain proxies: 2.84, per 1000 atoms: 0.22 Number of scatterers: 12748 At special positions: 0 Unit cell: (118.8, 123.2, 118.8, 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 245 15.00 O 2861 8.00 N 2378 7.00 C 7234 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: 1.06 Conformation dependent library (CDL) restraints added in 428.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 44 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 41 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 27 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 30 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 41 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 44 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 30 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 27 " Number of angles added : 12 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 60.1% alpha, 4.8% beta 120 base pairs and 188 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'L' and resid 59 through 68 removed outlier: 4.351A pdb=" N ALA L 63 " --> pdb=" O SER L 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.886A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.808A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.848A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.589A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.652A 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 45 through 73 removed outlier: 4.513A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.905A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.733A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.577A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.930A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.500A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.536A 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: 4.458A 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 35 through 46 Processing helix chain 'H' and resid 53 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.559A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 removed outlier: 4.072A 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 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 55 through 59 removed outlier: 3.603A pdb=" N ASP K 58 " --> pdb=" O THR K 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 34 removed outlier: 3.543A pdb=" N LYS O 27 " --> pdb=" O ILE O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 41 removed outlier: 4.170A pdb=" N GLN O 40 " --> pdb=" O PRO O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 59 removed outlier: 3.787A pdb=" N ASP O 58 " --> pdb=" O THR O 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.886A 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: 3.526A 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 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.338A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.016A 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 removed outlier: 3.534A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.502A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 12 through 14 removed outlier: 3.695A pdb=" N LEU K 69 " --> pdb=" O LYS K 6 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS K 68 " --> pdb=" O ILE K 44 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 13 through 14 removed outlier: 4.029A pdb=" N ILE O 13 " --> pdb=" O VAL O 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL O 5 " --> pdb=" O ILE O 13 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'O' and resid 43 through 45 removed outlier: 4.331A pdb=" N LEU O 43 " --> pdb=" O LEU O 50 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 309 hydrogen bonds 614 hydrogen bond angles 0 basepair planarities 120 basepair parallelities 188 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.41 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: 3184 1.34 - 1.46: 3614 1.46 - 1.58: 6130 1.58 - 1.70: 488 1.70 - 1.82: 40 Bond restraints: 13456 Sorted by residual: bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DG J 76 " pdb=" C2' DG J 76 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DG J 97 " pdb=" C2' DG J 97 " 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 1.06e+01 bond pdb=" C3' DC I 45 " pdb=" C2' DC I 45 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 13451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 18359 1.62 - 3.24: 813 3.24 - 4.86: 32 4.86 - 6.48: 4 6.48 - 8.10: 2 Bond angle restraints: 19210 Sorted by residual: angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " 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 50 " pdb=" C4 DT J 50 " pdb=" O4 DT J 50 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT I 57 " pdb=" C4 DT I 57 " pdb=" O4 DT I 57 " 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 J 35 " pdb=" C4 DT J 35 " pdb=" O4 DT J 35 " 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 46 " pdb=" C4 DT I 46 " pdb=" O4 DT I 46 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.84e+01 ... (remaining 19205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 6404 35.43 - 70.85: 1060 70.85 - 106.28: 29 106.28 - 141.71: 1 141.71 - 177.14: 3 Dihedral angle restraints: 7497 sinusoidal: 4670 harmonic: 2827 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 -140.00 37.14 -177.14 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 34.41 -174.41 1 3.50e+01 8.16e-04 1.56e+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 76.54 143.46 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 7494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1440 0.035 - 0.070: 551 0.070 - 0.106: 174 0.106 - 0.141: 35 0.141 - 0.176: 1 Chirality restraints: 2201 Sorted by residual: 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 -2.55 -0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA ILE K 36 " pdb=" N ILE K 36 " pdb=" C ILE K 36 " pdb=" CB ILE K 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" P DA I 5 " pdb=" OP1 DA I 5 " pdb=" OP2 DA I 5 " pdb=" O5' DA I 5 " both_signs ideal model delta sigma weight residual True 2.34 -2.47 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 2198 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU K 18 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.23e+00 pdb=" N PRO K 19 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO K 19 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO K 19 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT J 118 " 0.019 2.00e-02 2.50e+03 1.10e-02 3.04e+00 pdb=" N1 DT J 118 " -0.022 2.00e-02 2.50e+03 pdb=" C2 DT J 118 " 0.006 2.00e-02 2.50e+03 pdb=" O2 DT J 118 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DT J 118 " -0.012 2.00e-02 2.50e+03 pdb=" C4 DT J 118 " 0.009 2.00e-02 2.50e+03 pdb=" O4 DT J 118 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT J 118 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT J 118 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT J 118 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " 0.018 2.00e-02 2.50e+03 7.47e-03 1.67e+00 pdb=" N9 DG I 121 " -0.016 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " -0.001 2.00e-02 2.50e+03 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 367 2.69 - 3.24: 11053 3.24 - 3.79: 22292 3.79 - 4.35: 27658 4.35 - 4.90: 41200 Nonbonded interactions: 102570 Sorted by model distance: nonbonded pdb=" O2 DC I 95 " pdb=" N2 DG J 53 " model vdw 2.132 2.496 nonbonded pdb=" N MET O 1 " pdb=" O VAL O 17 " model vdw 2.157 3.120 nonbonded pdb=" O THR K 14 " pdb=" NZ LYS K 29 " model vdw 2.236 3.120 nonbonded pdb=" NE2 GLN K 40 " pdb=" O ARG K 72 " model vdw 2.270 3.120 nonbonded pdb=" NZ LYS B 91 " pdb=" OH TYR D 80 " model vdw 2.272 3.120 ... (remaining 102565 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 40 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 101) } 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 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: 0.890 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.470 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 0.038 13464 Z= 0.452 Angle : 0.662 8.104 19222 Z= 0.586 Chirality : 0.041 0.176 2201 Planarity : 0.003 0.057 1586 Dihedral : 25.724 177.136 5665 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % 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: 2.01 (0.28), residues: 951 helix: 2.58 (0.22), residues: 566 sheet: 1.59 (0.97), residues: 22 loop : -0.79 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 42 TYR 0.014 0.001 TYR G 50 PHE 0.017 0.001 PHE K 4 TRP 0.001 0.000 TRP N 25 HIS 0.001 0.000 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.45 (13456) covalent geometry : angle 0.65948 / 0.59 (19210) hydrogen bonds : bond 0.11563 / 7.79 ( 735) hydrogen bonds : angle 3.99125 / 2.92 ( 1871) metal coordination : bond 0.00210 / 0.14 ( 8) metal coordination : angle 2.35633 / 1.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.425 Fit side-chains REVERT: C 84 GLN cc_start: 0.8193 (tp-100) cc_final: 0.7922 (tp40) REVERT: E 59 GLU cc_start: 0.6945 (pp20) cc_final: 0.6552 (pp20) REVERT: F 63 GLU cc_start: 0.8106 (tt0) cc_final: 0.7172 (tp30) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1206 time to fit residues: 25.1315 Evaluate side-chains 118 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 30.0000 chunk 113 optimal weight: 30.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN D 46 HIS K 68 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.130778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.097733 restraints weight = 28585.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097638 restraints weight = 30841.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.097963 restraints weight = 29573.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098235 restraints weight = 26584.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.098292 restraints weight = 24761.240| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.004 0.043 13464 Z= 0.207 Angle : 0.658 8.119 19222 Z= 0.375 Chirality : 0.047 0.371 2201 Planarity : 0.005 0.052 1586 Dihedral : 29.291 177.398 3736 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.05 % Allowed : 9.76 % Favored : 88.19 % 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: 1.53 (0.28), residues: 951 helix: 2.18 (0.22), residues: 575 sheet: 0.95 (0.85), residues: 28 loop : -1.05 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 72 TYR 0.013 0.002 TYR C 50 PHE 0.042 0.003 PHE L 32 TRP 0.005 0.001 TRP L 25 HIS 0.006 0.002 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (13456) covalent geometry : angle 0.65394 / 0.37 (19210) hydrogen bonds : bond 0.06594 / 4.30 ( 735) hydrogen bonds : angle 3.42079 / 2.47 ( 1871) metal coordination : bond 0.00987 / 0.48 ( 8) metal coordination : angle 3.03898 / 1.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.299 Fit side-chains REVERT: E 123 ASP cc_start: 0.8957 (m-30) cc_final: 0.8748 (m-30) REVERT: F 63 GLU cc_start: 0.7919 (tt0) cc_final: 0.7633 (tp30) REVERT: O 49 GLN cc_start: 0.6457 (tm-30) cc_final: 0.5735 (pp30) REVERT: O 55 THR cc_start: 0.2486 (OUTLIER) cc_final: 0.1910 (p) outliers start: 17 outliers final: 9 residues processed: 140 average time/residue: 0.1103 time to fit residues: 22.0643 Evaluate side-chains 128 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain O residue 55 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 45 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 93 optimal weight: 50.0000 chunk 24 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 64 GLN K 31 GLN K 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.128908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.095938 restraints weight = 28618.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.096189 restraints weight = 29775.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.096366 restraints weight = 30950.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096666 restraints weight = 26894.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.096725 restraints weight = 24826.004| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13464 Z= 0.183 Angle : 0.621 8.465 19222 Z= 0.355 Chirality : 0.045 0.384 2201 Planarity : 0.005 0.100 1586 Dihedral : 29.622 176.121 3736 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.57 % Allowed : 14.22 % Favored : 84.22 % 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: 1.38 (0.28), residues: 951 helix: 2.10 (0.22), residues: 576 sheet: 0.97 (0.82), residues: 28 loop : -1.19 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 99 TYR 0.024 0.002 TYR H 39 PHE 0.053 0.002 PHE L 32 TRP 0.005 0.001 TRP N 25 HIS 0.006 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (13456) covalent geometry : angle 0.61501 / 0.36 (19210) hydrogen bonds : bond 0.06348 / 4.22 ( 735) hydrogen bonds : angle 3.32056 / 2.38 ( 1871) metal coordination : bond 0.00886 / 0.43 ( 8) metal coordination : angle 3.41567 / 1.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: B 52 GLU cc_start: 0.6839 (pm20) cc_final: 0.6479 (mp0) REVERT: B 84 MET cc_start: 0.8135 (tpp) cc_final: 0.7895 (tpp) REVERT: B 88 TYR cc_start: 0.8098 (m-80) cc_final: 0.7521 (m-80) REVERT: B 91 LYS cc_start: 0.7866 (ttpt) cc_final: 0.7665 (ttpt) REVERT: E 123 ASP cc_start: 0.8906 (m-30) cc_final: 0.8686 (m-30) REVERT: F 63 GLU cc_start: 0.7781 (tt0) cc_final: 0.7465 (tp30) REVERT: O 49 GLN cc_start: 0.6483 (tm-30) cc_final: 0.5858 (pp30) REVERT: O 55 THR cc_start: 0.2187 (OUTLIER) cc_final: 0.1663 (p) outliers start: 13 outliers final: 10 residues processed: 135 average time/residue: 0.1163 time to fit residues: 22.7154 Evaluate side-chains 130 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 55 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 51 optimal weight: 0.9980 chunk 34 optimal weight: 0.0050 chunk 67 optimal weight: 4.9990 chunk 114 optimal weight: 30.0000 chunk 76 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 106 optimal weight: 50.0000 chunk 98 optimal weight: 30.0000 chunk 42 optimal weight: 9.9990 chunk 101 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 overall best weight: 2.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.128798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095255 restraints weight = 28534.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.095407 restraints weight = 32129.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.095686 restraints weight = 30055.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.095957 restraints weight = 27775.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.095959 restraints weight = 26252.115| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13464 Z= 0.162 Angle : 0.595 8.445 19222 Z= 0.341 Chirality : 0.043 0.388 2201 Planarity : 0.005 0.062 1586 Dihedral : 29.694 176.899 3736 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.05 % Allowed : 15.54 % Favored : 82.41 % 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: 1.47 (0.28), residues: 951 helix: 2.21 (0.22), residues: 576 sheet: 0.69 (0.80), residues: 29 loop : -1.21 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 33 TYR 0.023 0.001 TYR H 39 PHE 0.059 0.002 PHE L 32 TRP 0.004 0.001 TRP N 25 HIS 0.005 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (13456) covalent geometry : angle 0.59064 / 0.34 (19210) hydrogen bonds : bond 0.06001 / 3.96 ( 735) hydrogen bonds : angle 3.21374 / 2.30 ( 1871) metal coordination : bond 0.00743 / 0.36 ( 8) metal coordination : angle 2.87752 / 1.65 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.380 Fit side-chains REVERT: B 52 GLU cc_start: 0.6920 (pm20) cc_final: 0.6679 (mp0) REVERT: E 123 ASP cc_start: 0.8786 (m-30) cc_final: 0.8573 (m-30) REVERT: F 63 GLU cc_start: 0.8010 (tt0) cc_final: 0.7677 (tp30) REVERT: O 49 GLN cc_start: 0.6484 (tm-30) cc_final: 0.5876 (pp30) outliers start: 17 outliers final: 15 residues processed: 135 average time/residue: 0.1167 time to fit residues: 22.9204 Evaluate side-chains 132 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain O residue 14 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 106 optimal weight: 50.0000 chunk 10 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 107 optimal weight: 30.0000 chunk 55 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 116 optimal weight: 50.0000 chunk 23 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.127825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.094400 restraints weight = 28446.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.094704 restraints weight = 30176.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.094840 restraints weight = 29435.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.095177 restraints weight = 26517.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.095182 restraints weight = 24595.502| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13464 Z= 0.178 Angle : 0.622 8.462 19222 Z= 0.351 Chirality : 0.044 0.391 2201 Planarity : 0.005 0.076 1586 Dihedral : 29.818 176.349 3736 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.53 % Allowed : 16.14 % Favored : 81.33 % 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: 1.28 (0.28), residues: 951 helix: 2.08 (0.22), residues: 576 sheet: 0.37 (0.76), residues: 31 loop : -1.32 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 33 TYR 0.024 0.002 TYR H 39 PHE 0.054 0.002 PHE L 32 TRP 0.004 0.001 TRP N 25 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.18 (13456) covalent geometry : angle 0.61635 / 0.35 (19210) hydrogen bonds : bond 0.06285 / 4.17 ( 735) hydrogen bonds : angle 3.26862 / 2.33 ( 1871) metal coordination : bond 0.00911 / 0.44 ( 8) metal coordination : angle 3.39626 / 1.95 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.330 Fit side-chains REVERT: B 52 GLU cc_start: 0.7003 (pm20) cc_final: 0.6673 (mp0) REVERT: B 88 TYR cc_start: 0.8235 (m-80) cc_final: 0.7619 (m-80) REVERT: E 123 ASP cc_start: 0.8792 (m-30) cc_final: 0.8592 (m-30) REVERT: F 63 GLU cc_start: 0.7994 (tt0) cc_final: 0.7714 (tp30) REVERT: O 49 GLN cc_start: 0.6410 (tm-30) cc_final: 0.5818 (pp30) outliers start: 21 outliers final: 15 residues processed: 134 average time/residue: 0.1157 time to fit residues: 22.3238 Evaluate side-chains 131 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 3 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 16 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 100 optimal weight: 30.0000 chunk 109 optimal weight: 20.0000 chunk 106 optimal weight: 50.0000 chunk 26 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 HIS 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 = 0.125563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.092528 restraints weight = 27957.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.092627 restraints weight = 28117.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.092823 restraints weight = 28780.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.093063 restraints weight = 26296.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.093021 restraints weight = 25474.050| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13464 Z= 0.236 Angle : 0.707 8.412 19222 Z= 0.390 Chirality : 0.048 0.391 2201 Planarity : 0.006 0.076 1586 Dihedral : 30.037 176.476 3736 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.77 % Allowed : 16.75 % Favored : 80.48 % 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: 0.68 (0.27), residues: 951 helix: 1.67 (0.22), residues: 572 sheet: -0.21 (0.79), residues: 32 loop : -1.63 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 33 TYR 0.016 0.002 TYR D 39 PHE 0.057 0.003 PHE L 32 TRP 0.008 0.001 TRP N 25 HIS 0.006 0.002 HIS G 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.24 (13456) covalent geometry : angle 0.70182 / 0.39 (19210) hydrogen bonds : bond 0.07609 / 4.98 ( 735) hydrogen bonds : angle 3.54101 / 2.52 ( 1871) metal coordination : bond 0.01175 / 0.57 ( 8) metal coordination : angle 3.51128 / 2.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.341 Fit side-chains REVERT: B 52 GLU cc_start: 0.7182 (pm20) cc_final: 0.6811 (mp0) REVERT: B 88 TYR cc_start: 0.8254 (m-80) cc_final: 0.7633 (m-80) REVERT: O 49 GLN cc_start: 0.6518 (tm-30) cc_final: 0.5914 (pp30) outliers start: 23 outliers final: 21 residues processed: 133 average time/residue: 0.1071 time to fit residues: 20.6728 Evaluate side-chains 137 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain O residue 12 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 93 optimal weight: 50.0000 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 99 optimal weight: 30.0000 chunk 87 optimal weight: 0.0670 chunk 60 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.127200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.093582 restraints weight = 27992.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.093796 restraints weight = 28467.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.094760 restraints weight = 26877.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.094762 restraints weight = 25380.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.094775 restraints weight = 21757.237| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13464 Z= 0.160 Angle : 0.619 8.322 19222 Z= 0.351 Chirality : 0.044 0.393 2201 Planarity : 0.005 0.077 1586 Dihedral : 29.971 176.935 3736 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.65 % Allowed : 17.47 % Favored : 79.88 % 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: 1.10 (0.28), residues: 951 helix: 2.02 (0.22), residues: 573 sheet: -0.24 (0.75), residues: 31 loop : -1.47 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 33 TYR 0.014 0.001 TYR H 39 PHE 0.042 0.002 PHE L 32 TRP 0.004 0.001 TRP N 25 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (13456) covalent geometry : angle 0.61490 / 0.35 (19210) hydrogen bonds : bond 0.06267 / 4.16 ( 735) hydrogen bonds : angle 3.27138 / 2.34 ( 1871) metal coordination : bond 0.00849 / 0.42 ( 8) metal coordination : angle 2.96229 / 1.79 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.223 Fit side-chains REVERT: B 52 GLU cc_start: 0.7092 (pm20) cc_final: 0.6760 (mp0) REVERT: B 88 TYR cc_start: 0.8168 (m-80) cc_final: 0.7462 (m-80) REVERT: B 91 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7632 (tptp) REVERT: H 73 GLU cc_start: 0.8160 (tp30) cc_final: 0.7931 (tp30) REVERT: K 40 GLN cc_start: 0.6292 (tp40) cc_final: 0.5882 (tp40) REVERT: K 56 LEU cc_start: 0.6531 (pp) cc_final: 0.6220 (pt) REVERT: O 49 GLN cc_start: 0.6437 (tm-30) cc_final: 0.5877 (pp30) outliers start: 22 outliers final: 20 residues processed: 138 average time/residue: 0.1085 time to fit residues: 21.6811 Evaluate side-chains 140 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain O residue 12 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 44 optimal weight: 0.0010 chunk 45 optimal weight: 0.8980 chunk 85 optimal weight: 0.1980 chunk 57 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.130020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.096396 restraints weight = 28128.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.097074 restraints weight = 26864.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.097145 restraints weight = 22899.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.097309 restraints weight = 20491.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.097674 restraints weight = 18701.649| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13464 Z= 0.128 Angle : 0.577 8.249 19222 Z= 0.334 Chirality : 0.042 0.388 2201 Planarity : 0.004 0.068 1586 Dihedral : 29.816 177.712 3736 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.33 % Allowed : 18.92 % Favored : 79.76 % 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: 1.63 (0.28), residues: 951 helix: 2.48 (0.22), residues: 574 sheet: -0.41 (0.72), residues: 31 loop : -1.30 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 33 TYR 0.011 0.001 TYR H 37 PHE 0.031 0.002 PHE N 32 TRP 0.004 0.001 TRP L 25 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.13 (13456) covalent geometry : angle 0.57221 / 0.33 (19210) hydrogen bonds : bond 0.04868 / 3.27 ( 735) hydrogen bonds : angle 2.93226 / 2.11 ( 1871) metal coordination : bond 0.00421 / 0.21 ( 8) metal coordination : angle 2.87746 / 1.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.358 Fit side-chains REVERT: B 88 TYR cc_start: 0.8108 (m-80) cc_final: 0.7409 (m-80) REVERT: D 68 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7150 (mt-10) REVERT: E 123 ASP cc_start: 0.8728 (m-30) cc_final: 0.8464 (m-30) REVERT: F 63 GLU cc_start: 0.7852 (tt0) cc_final: 0.7568 (tp30) REVERT: H 73 GLU cc_start: 0.8146 (tp30) cc_final: 0.7798 (tp30) REVERT: K 22 THR cc_start: 0.5189 (t) cc_final: 0.4774 (p) REVERT: K 40 GLN cc_start: 0.5925 (tp40) cc_final: 0.5543 (tp40) REVERT: O 49 GLN cc_start: 0.6569 (tm-30) cc_final: 0.5965 (pp30) outliers start: 11 outliers final: 10 residues processed: 136 average time/residue: 0.1078 time to fit residues: 21.2991 Evaluate side-chains 134 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 109 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.126925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093119 restraints weight = 27923.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.093583 restraints weight = 28942.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.093672 restraints weight = 27950.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.093958 restraints weight = 25668.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.093925 restraints weight = 23459.783| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13464 Z= 0.201 Angle : 0.643 9.994 19222 Z= 0.358 Chirality : 0.045 0.390 2201 Planarity : 0.005 0.071 1586 Dihedral : 29.950 176.452 3736 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.57 % Allowed : 19.40 % Favored : 79.04 % 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: 1.17 (0.28), residues: 951 helix: 2.07 (0.22), residues: 576 sheet: -0.47 (0.70), residues: 31 loop : -1.44 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 92 TYR 0.012 0.002 TYR H 39 PHE 0.028 0.002 PHE L 32 TRP 0.003 0.001 TRP N 25 HIS 0.005 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (13456) covalent geometry : angle 0.63776 / 0.36 (19210) hydrogen bonds : bond 0.06422 / 4.23 ( 735) hydrogen bonds : angle 3.22681 / 2.31 ( 1871) metal coordination : bond 0.00883 / 0.45 ( 8) metal coordination : angle 3.30973 / 1.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.328 Fit side-chains REVERT: B 88 TYR cc_start: 0.8175 (m-80) cc_final: 0.7493 (m-80) REVERT: E 123 ASP cc_start: 0.8880 (m-30) cc_final: 0.8629 (m-30) REVERT: E 133 GLU cc_start: 0.6389 (pm20) cc_final: 0.6020 (pm20) REVERT: O 49 GLN cc_start: 0.6603 (tm-30) cc_final: 0.5987 (pp30) REVERT: O 71 LEU cc_start: 0.4469 (OUTLIER) cc_final: 0.3516 (tp) outliers start: 13 outliers final: 12 residues processed: 127 average time/residue: 0.1071 time to fit residues: 19.8030 Evaluate side-chains 129 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 ILE Chi-restraints excluded: chain O residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.5980 chunk 110 optimal weight: 30.0000 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.128246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.094330 restraints weight = 28140.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.094889 restraints weight = 29281.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095099 restraints weight = 26277.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.095373 restraints weight = 23999.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.095386 restraints weight = 22226.698| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13464 Z= 0.137 Angle : 0.592 10.425 19222 Z= 0.338 Chirality : 0.043 0.388 2201 Planarity : 0.004 0.071 1586 Dihedral : 29.918 176.658 3736 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.57 % Allowed : 19.64 % Favored : 78.80 % 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: 1.39 (0.28), residues: 951 helix: 2.29 (0.22), residues: 574 sheet: -0.52 (0.72), residues: 31 loop : -1.40 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 92 TYR 0.012 0.001 TYR H 39 PHE 0.026 0.002 PHE N 32 TRP 0.003 0.000 TRP N 25 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (13456) covalent geometry : angle 0.58817 / 0.34 (19210) hydrogen bonds : bond 0.05598 / 3.71 ( 735) hydrogen bonds : angle 3.07369 / 2.21 ( 1871) metal coordination : bond 0.00604 / 0.32 ( 8) metal coordination : angle 2.82610 / 1.69 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.289 Fit side-chains REVERT: B 88 TYR cc_start: 0.8161 (m-80) cc_final: 0.7490 (m-80) REVERT: E 123 ASP cc_start: 0.8794 (m-30) cc_final: 0.8554 (m-30) REVERT: H 73 GLU cc_start: 0.8087 (tp30) cc_final: 0.7801 (tp30) REVERT: O 49 GLN cc_start: 0.6653 (tm-30) cc_final: 0.6036 (pp30) outliers start: 13 outliers final: 12 residues processed: 128 average time/residue: 0.1059 time to fit residues: 19.7664 Evaluate side-chains 127 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 26 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 109 optimal weight: 30.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.127101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.093042 restraints weight = 27971.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.093386 restraints weight = 28828.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094000 restraints weight = 25327.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.093946 restraints weight = 24741.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.094148 restraints weight = 21727.808| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13464 Z= 0.178 Angle : 0.628 9.834 19222 Z= 0.352 Chirality : 0.044 0.386 2201 Planarity : 0.005 0.071 1586 Dihedral : 29.966 176.308 3736 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.81 % Allowed : 19.40 % Favored : 78.80 % 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: 1.18 (0.28), residues: 951 helix: 2.12 (0.22), residues: 572 sheet: -0.35 (0.73), residues: 30 loop : -1.48 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 92 TYR 0.014 0.001 TYR H 80 PHE 0.026 0.002 PHE N 32 TRP 0.003 0.001 TRP N 25 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.18 (13456) covalent geometry : angle 0.62308 / 0.35 (19210) hydrogen bonds : bond 0.06215 / 4.09 ( 735) hydrogen bonds : angle 3.20038 / 2.29 ( 1871) metal coordination : bond 0.00789 / 0.40 ( 8) metal coordination : angle 3.19184 / 1.84 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1572.85 seconds wall clock time: 27 minutes 53.66 seconds (1673.66 seconds total)