Starting phenix.real_space_refine on Wed Aug 5 23:09:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6s_29781/08_2026/8g6s_29781.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6s_29781/08_2026/8g6s_29781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g6s_29781/08_2026/8g6s_29781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6s_29781/08_2026/8g6s_29781.map" model { file = "/net/cci-nas-00/data/ceres_data/8g6s_29781/08_2026/8g6s_29781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6s_29781/08_2026/8g6s_29781.cif" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 13 5.16 5 C 6944 2.51 5 N 2330 2.21 5 O 2905 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 12480 Number of models: 1 Model: "" Number of chains: 11 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: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU K 73 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.80 Time building chain proxies: 3.26, per 1000 atoms: 0.26 Number of scatterers: 12480 At special positions: 0 Unit cell: (125.13, 81.48, 132.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 288 15.00 O 2905 8.00 N 2330 7.00 C 6944 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: 1.23 Conformation dependent library (CDL) restraints added in 451.7 milliseconds 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 11 sheets defined 69.5% alpha, 4.6% beta 142 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.996A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.621A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.035A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.549A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.583A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.578A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.597A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.591A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.538A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.774A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.606A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 77 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.686A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.677A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.765A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.599A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.644A 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 100 through 121 removed outlier: 3.754A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 35 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 60 removed outlier: 3.547A pdb=" N TYR K 59 " --> pdb=" O LEU K 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.980A 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: 3.891A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.307A 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: 6.980A 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: 3.760A 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: 7.307A 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 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 12 through 16 removed outlier: 8.767A pdb=" N LEU K 67 " --> pdb=" O GLN K 2 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE K 4 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU K 69 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS K 6 " --> pdb=" O LEU K 69 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU K 71 " --> pdb=" O LYS K 6 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 726 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 1.60 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: 2894 1.34 - 1.46: 4157 1.46 - 1.58: 5637 1.58 - 1.70: 576 1.70 - 1.82: 24 Bond restraints: 13288 Sorted by residual: bond pdb=" C3' DC J 24 " pdb=" C2' DC J 24 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.47e+01 bond pdb=" C3' DG I -30 " pdb=" C2' DG I -30 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.34e+01 bond pdb=" C3' DT J 54 " pdb=" C2' DT J 54 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DC I -29 " pdb=" C2' DC I -29 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 ... (remaining 13283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 18284 1.79 - 3.58: 865 3.58 - 5.37: 34 5.37 - 7.17: 6 7.17 - 8.96: 3 Bond angle restraints: 19192 Sorted by residual: angle pdb=" N3 DT I -17 " pdb=" C4 DT I -17 " pdb=" O4 DT I -17 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT J 22 " pdb=" C4 DT J 22 " pdb=" O4 DT J 22 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT J -50 " pdb=" C4 DT J -50 " pdb=" O4 DT J -50 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT I -43 " pdb=" C4 DT I -43 " pdb=" O4 DT I -43 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 19187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 5817 34.50 - 69.00: 1426 69.00 - 103.50: 17 103.50 - 138.00: 3 138.00 - 172.50: 1 Dihedral angle restraints: 7264 sinusoidal: 4874 harmonic: 2390 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 47.50 172.50 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 86.15 133.85 1 3.50e+01 8.16e-04 1.33e+01 dihedral pdb=" C4' DA J -38 " pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " pdb=" P DG J -37 " ideal model delta sinusoidal sigma weight residual 220.00 93.09 126.91 1 3.50e+01 8.16e-04 1.25e+01 ... (remaining 7261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1051 0.027 - 0.053: 723 0.053 - 0.080: 235 0.080 - 0.107: 143 0.107 - 0.133: 41 Chirality restraints: 2193 Sorted by residual: chirality pdb=" CB ILE D 86 " pdb=" CA ILE D 86 " pdb=" CG1 ILE D 86 " pdb=" CG2 ILE D 86 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE C 111 " pdb=" N ILE C 111 " pdb=" C ILE C 111 " pdb=" CB ILE C 111 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE G 111 " pdb=" N ILE G 111 " pdb=" C ILE G 111 " pdb=" CB ILE G 111 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 2190 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 112 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.18e+00 pdb=" C ILE E 112 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE E 112 " -0.019 2.00e-02 2.50e+03 pdb=" N HIS E 113 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 80 " 0.012 2.00e-02 2.50e+03 1.24e-02 3.08e+00 pdb=" CG TYR H 80 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR H 80 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR H 80 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR H 80 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 80 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR H 80 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 80 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " -0.022 2.00e-02 2.50e+03 9.22e-03 2.55e+00 pdb=" N9 DG I 26 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.002 2.00e-02 2.50e+03 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 449 2.70 - 3.25: 10994 3.25 - 3.80: 22410 3.80 - 4.35: 26841 4.35 - 4.90: 39404 Nonbonded interactions: 100098 Sorted by model distance: nonbonded pdb=" N GLU H 102 " pdb=" OE1 GLU H 102 " model vdw 2.149 3.120 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 75 " model vdw 2.212 3.040 nonbonded pdb=" N GLU G 41 " pdb=" OE1 GLU G 41 " model vdw 2.232 3.120 nonbonded pdb=" OG1 THR F 82 " pdb=" OD2 ASP F 85 " model vdw 2.255 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 75 " model vdw 2.258 3.040 ... (remaining 100093 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 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.80 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.770 Find NCS groups from input model: 0.150 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 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 : 0.006 0.036 13288 Z= 0.512 Angle : 0.755 8.958 19192 Z= 0.652 Chirality : 0.043 0.133 2193 Planarity : 0.004 0.034 1426 Dihedral : 27.639 172.505 5720 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.43 % Allowed : 24.86 % Favored : 74.71 % 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: 2.29 (0.30), residues: 806 helix: 2.56 (0.23), residues: 532 sheet: 1.56 (1.03), residues: 26 loop : -0.91 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 71 TYR 0.029 0.001 TYR H 80 PHE 0.009 0.001 PHE E 78 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.51 (13288) covalent geometry : angle 0.75500 / 0.65 (19192) hydrogen bonds : bond 0.11320 / 7.91 ( 775) hydrogen bonds : angle 4.30020 / 3.07 ( 1944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8514 (tp30) cc_final: 0.8208 (tp30) REVERT: C 64 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8042 (tt0) REVERT: C 99 ARG cc_start: 0.7998 (mmt180) cc_final: 0.7427 (mtp85) REVERT: D 48 ASP cc_start: 0.9145 (p0) cc_final: 0.8562 (p0) REVERT: E 42 ARG cc_start: 0.8779 (mmm-85) cc_final: 0.8273 (mtp85) REVERT: G 95 LYS cc_start: 0.8517 (tptp) cc_final: 0.8116 (ttmm) REVERT: G 99 ARG cc_start: 0.7820 (mmt-90) cc_final: 0.6968 (mtp85) REVERT: K 1 MET cc_start: 0.7299 (ppp) cc_final: 0.6868 (ppp) REVERT: K 48 LYS cc_start: 0.6017 (mmtt) cc_final: 0.5610 (mmtt) outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.1455 time to fit residues: 25.7939 Evaluate side-chains 120 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.0970 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN C 38 ASN G 73 ASN K 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.099436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.067304 restraints weight = 34061.218| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.38 r_work: 0.2840 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13288 Z= 0.156 Angle : 0.608 10.506 19192 Z= 0.368 Chirality : 0.042 0.218 2193 Planarity : 0.004 0.035 1426 Dihedral : 29.992 174.649 4087 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.30 % Allowed : 23.70 % Favored : 75.00 % 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: 2.53 (0.30), residues: 806 helix: 2.69 (0.22), residues: 544 sheet: 1.45 (1.04), residues: 26 loop : -0.82 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 71 TYR 0.024 0.001 TYR H 80 PHE 0.013 0.001 PHE K 4 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.16 (13288) covalent geometry : angle 0.60774 / 0.37 (19192) hydrogen bonds : bond 0.06355 / 4.30 ( 775) hydrogen bonds : angle 3.37189 / 2.38 ( 1944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8755 (tp30) cc_final: 0.8495 (tp30) REVERT: B 84 MET cc_start: 0.8052 (tpp) cc_final: 0.7674 (mmm) REVERT: B 93 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7490 (mt0) REVERT: C 64 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8446 (tt0) REVERT: D 48 ASP cc_start: 0.9073 (p0) cc_final: 0.8518 (p0) REVERT: E 73 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8665 (tm-30) REVERT: F 27 GLN cc_start: 0.8679 (tp40) cc_final: 0.8470 (tm-30) REVERT: F 59 LYS cc_start: 0.9408 (ttpt) cc_final: 0.9180 (ttpp) REVERT: G 95 LYS cc_start: 0.8647 (tptp) cc_final: 0.8267 (ttmm) REVERT: G 99 ARG cc_start: 0.8206 (mmt-90) cc_final: 0.7546 (mtp85) REVERT: H 117 LYS cc_start: 0.9035 (tptm) cc_final: 0.8594 (ttpt) outliers start: 9 outliers final: 6 residues processed: 139 average time/residue: 0.1287 time to fit residues: 24.8747 Evaluate side-chains 128 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.098620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.066103 restraints weight = 34160.422| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.39 r_work: 0.2813 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13288 Z= 0.157 Angle : 0.586 9.864 19192 Z= 0.355 Chirality : 0.041 0.213 2193 Planarity : 0.004 0.034 1426 Dihedral : 30.044 175.289 4085 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.88 % Allowed : 24.86 % Favored : 73.27 % 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: 2.73 (0.30), residues: 806 helix: 2.93 (0.22), residues: 540 sheet: 1.43 (1.08), residues: 26 loop : -0.92 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 55 TYR 0.032 0.001 TYR H 80 PHE 0.011 0.001 PHE K 4 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.16 (13288) covalent geometry : angle 0.58631 / 0.36 (19192) hydrogen bonds : bond 0.06135 / 4.13 ( 775) hydrogen bonds : angle 3.17578 / 2.23 ( 1944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8767 (tp30) cc_final: 0.8482 (tp30) REVERT: C 64 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8388 (tt0) REVERT: C 91 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7671 (tm-30) REVERT: C 92 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8394 (mm-30) REVERT: E 73 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8553 (tt0) REVERT: G 95 LYS cc_start: 0.8673 (tptp) cc_final: 0.8279 (ttmm) REVERT: G 99 ARG cc_start: 0.8242 (mmt-90) cc_final: 0.7550 (mtp85) REVERT: G 102 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8529 (mt) REVERT: H 117 LYS cc_start: 0.9032 (tptm) cc_final: 0.8597 (ttpt) outliers start: 13 outliers final: 5 residues processed: 132 average time/residue: 0.1218 time to fit residues: 22.7451 Evaluate side-chains 125 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 24 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.098533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.066063 restraints weight = 34003.501| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.37 r_work: 0.2812 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13288 Z= 0.153 Angle : 0.577 9.722 19192 Z= 0.349 Chirality : 0.041 0.219 2193 Planarity : 0.004 0.034 1426 Dihedral : 30.043 175.984 4085 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.46 % Allowed : 24.86 % Favored : 72.69 % 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: 2.80 (0.30), residues: 806 helix: 3.00 (0.22), residues: 540 sheet: 1.43 (1.08), residues: 26 loop : -0.94 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 63 TYR 0.039 0.002 TYR H 80 PHE 0.009 0.001 PHE K 4 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (13288) covalent geometry : angle 0.57738 / 0.35 (19192) hydrogen bonds : bond 0.05882 / 3.95 ( 775) hydrogen bonds : angle 3.08450 / 2.16 ( 1944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8735 (tp30) cc_final: 0.8421 (tp30) REVERT: B 93 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7590 (mt0) REVERT: C 64 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8404 (tt0) REVERT: E 73 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8506 (tt0) REVERT: G 95 LYS cc_start: 0.8674 (tptp) cc_final: 0.8277 (ttmm) REVERT: G 99 ARG cc_start: 0.8205 (mmt-90) cc_final: 0.7510 (mtp85) REVERT: K 67 LEU cc_start: 0.9241 (tt) cc_final: 0.8569 (mp) outliers start: 17 outliers final: 9 residues processed: 133 average time/residue: 0.1214 time to fit residues: 22.8397 Evaluate side-chains 128 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 0.0970 chunk 91 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS C 38 ASN H 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.097961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.065310 restraints weight = 34028.976| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.36 r_work: 0.2794 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (26 function evaluations) r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13288 Z= 0.161 Angle : 0.581 9.395 19192 Z= 0.350 Chirality : 0.041 0.221 2193 Planarity : 0.004 0.035 1426 Dihedral : 30.016 177.383 4085 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.18 % Allowed : 24.42 % Favored : 72.40 % 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: 2.80 (0.30), residues: 806 helix: 3.00 (0.22), residues: 540 sheet: 1.40 (1.08), residues: 26 loop : -0.93 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 42 TYR 0.039 0.001 TYR H 80 PHE 0.009 0.001 PHE K 4 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (13288) covalent geometry : angle 0.58135 / 0.35 (19192) hydrogen bonds : bond 0.06066 / 4.06 ( 775) hydrogen bonds : angle 3.11086 / 2.18 ( 1944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8731 (tp30) cc_final: 0.8444 (tp30) REVERT: B 93 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7665 (mt0) REVERT: C 64 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8434 (tt0) REVERT: C 91 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7625 (tm-30) REVERT: C 92 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8543 (mm-30) REVERT: D 39 TYR cc_start: 0.8449 (t80) cc_final: 0.8193 (t80) REVERT: E 73 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8543 (tt0) REVERT: G 95 LYS cc_start: 0.8718 (tptp) cc_final: 0.8327 (ttmm) REVERT: G 99 ARG cc_start: 0.8261 (mmt-90) cc_final: 0.7589 (mtp85) REVERT: K 1 MET cc_start: 0.6932 (ppp) cc_final: 0.6352 (ppp) outliers start: 22 outliers final: 14 residues processed: 138 average time/residue: 0.1148 time to fit residues: 22.2353 Evaluate side-chains 131 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN H 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.098760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.066298 restraints weight = 33734.179| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.35 r_work: 0.2815 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13288 Z= 0.142 Angle : 0.566 8.883 19192 Z= 0.344 Chirality : 0.040 0.225 2193 Planarity : 0.004 0.039 1426 Dihedral : 29.995 177.850 4085 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.60 % Allowed : 26.01 % Favored : 71.39 % 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: 2.87 (0.30), residues: 806 helix: 3.08 (0.22), residues: 543 sheet: 1.06 (1.04), residues: 26 loop : -0.96 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 54 TYR 0.028 0.001 TYR H 80 PHE 0.009 0.001 PHE K 4 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.14 (13288) covalent geometry : angle 0.56639 / 0.34 (19192) hydrogen bonds : bond 0.05613 / 3.77 ( 775) hydrogen bonds : angle 2.99880 / 2.10 ( 1944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8697 (tp30) cc_final: 0.8402 (tp30) REVERT: B 93 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7578 (mt0) REVERT: C 64 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8406 (tt0) REVERT: C 92 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8461 (mm-30) REVERT: D 39 TYR cc_start: 0.8404 (t80) cc_final: 0.8153 (t80) REVERT: E 73 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8506 (tt0) REVERT: F 47 SER cc_start: 0.8611 (t) cc_final: 0.8379 (t) REVERT: G 95 LYS cc_start: 0.8684 (tptp) cc_final: 0.8295 (ttmm) REVERT: G 99 ARG cc_start: 0.8237 (mmt-90) cc_final: 0.7552 (mtp85) outliers start: 18 outliers final: 13 residues processed: 139 average time/residue: 0.1174 time to fit residues: 23.0241 Evaluate side-chains 133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 0.0270 chunk 72 optimal weight: 30.0000 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 71 optimal weight: 30.0000 chunk 19 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN H 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.098230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.065807 restraints weight = 33859.516| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.35 r_work: 0.2802 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (19 function evaluations) r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13288 Z= 0.153 Angle : 0.576 8.761 19192 Z= 0.347 Chirality : 0.041 0.227 2193 Planarity : 0.004 0.043 1426 Dihedral : 29.991 178.898 4085 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.60 % Allowed : 25.43 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 2.85 (0.30), residues: 806 helix: 3.10 (0.22), residues: 540 sheet: 1.02 (1.04), residues: 26 loop : -1.01 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 54 TYR 0.029 0.001 TYR H 80 PHE 0.008 0.001 PHE K 4 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (13288) covalent geometry : angle 0.57573 / 0.35 (19192) hydrogen bonds : bond 0.05738 / 3.85 ( 775) hydrogen bonds : angle 3.02017 / 2.11 ( 1944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8703 (tp30) cc_final: 0.8429 (tp30) REVERT: B 93 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7643 (mt0) REVERT: C 64 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8427 (tt0) REVERT: C 91 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7569 (tm-30) REVERT: C 92 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8517 (mm-30) REVERT: D 39 TYR cc_start: 0.8473 (t80) cc_final: 0.8229 (t80) REVERT: E 73 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8535 (tt0) REVERT: G 95 LYS cc_start: 0.8721 (tptp) cc_final: 0.8330 (ttmm) REVERT: G 99 ARG cc_start: 0.8281 (mmt-90) cc_final: 0.7623 (mtp85) REVERT: K 1 MET cc_start: 0.7024 (ppp) cc_final: 0.6560 (ppp) outliers start: 18 outliers final: 14 residues processed: 135 average time/residue: 0.1202 time to fit residues: 22.9895 Evaluate side-chains 132 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain K residue 4 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 3 optimal weight: 0.6980 chunk 102 optimal weight: 0.0670 chunk 78 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 53 optimal weight: 0.0570 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN H 92 GLN ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.099516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.067349 restraints weight = 33910.459| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.36 r_work: 0.2840 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13288 Z= 0.138 Angle : 0.565 8.289 19192 Z= 0.342 Chirality : 0.040 0.229 2193 Planarity : 0.004 0.057 1426 Dihedral : 29.961 179.727 4085 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.31 % Allowed : 26.16 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 2.93 (0.30), residues: 806 helix: 3.14 (0.22), residues: 543 sheet: 0.80 (1.03), residues: 26 loop : -0.95 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 35 TYR 0.024 0.001 TYR H 80 PHE 0.010 0.001 PHE K 4 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.14 (13288) covalent geometry : angle 0.56498 / 0.34 (19192) hydrogen bonds : bond 0.05225 / 3.52 ( 775) hydrogen bonds : angle 2.91647 / 2.03 ( 1944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8671 (tp30) cc_final: 0.8417 (tp30) REVERT: B 93 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7473 (mt0) REVERT: C 64 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8413 (tt0) REVERT: C 91 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7506 (tm-30) REVERT: C 92 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8504 (mm-30) REVERT: D 39 TYR cc_start: 0.8385 (t80) cc_final: 0.8148 (t80) REVERT: E 73 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8566 (tt0) REVERT: F 47 SER cc_start: 0.8552 (t) cc_final: 0.8295 (t) REVERT: F 88 TYR cc_start: 0.8193 (m-10) cc_final: 0.7951 (m-10) REVERT: G 95 LYS cc_start: 0.8643 (tptp) cc_final: 0.8218 (ttmm) REVERT: G 99 ARG cc_start: 0.8226 (mmt-90) cc_final: 0.7547 (mtp85) REVERT: K 1 MET cc_start: 0.6926 (ppp) cc_final: 0.6405 (ppp) outliers start: 16 outliers final: 12 residues processed: 139 average time/residue: 0.1161 time to fit residues: 23.1305 Evaluate side-chains 137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 96 optimal weight: 20.0000 chunk 34 optimal weight: 0.0370 chunk 43 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN E 76 GLN H 92 GLN ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.099575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.067531 restraints weight = 33880.242| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.36 r_work: 0.2842 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13288 Z= 0.140 Angle : 0.569 7.789 19192 Z= 0.343 Chirality : 0.040 0.229 2193 Planarity : 0.004 0.048 1426 Dihedral : 29.958 178.620 4085 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.75 % Allowed : 26.16 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 2.88 (0.30), residues: 806 helix: 3.10 (0.22), residues: 543 sheet: 0.73 (1.04), residues: 26 loop : -0.96 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 54 TYR 0.011 0.001 TYR F 88 PHE 0.012 0.001 PHE K 4 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.14 (13288) covalent geometry : angle 0.56862 / 0.34 (19192) hydrogen bonds : bond 0.05230 / 3.52 ( 775) hydrogen bonds : angle 2.94004 / 2.06 ( 1944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8686 (tp30) cc_final: 0.8440 (tp30) REVERT: B 93 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7494 (mt0) REVERT: C 64 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8407 (tt0) REVERT: C 92 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8499 (mm-30) REVERT: D 39 TYR cc_start: 0.8399 (t80) cc_final: 0.8160 (t80) REVERT: E 73 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8564 (tt0) REVERT: G 95 LYS cc_start: 0.8637 (tptp) cc_final: 0.8217 (ttmm) REVERT: G 99 ARG cc_start: 0.8238 (mmt-90) cc_final: 0.7565 (mtp85) REVERT: K 1 MET cc_start: 0.6881 (ppp) cc_final: 0.6309 (ppp) outliers start: 19 outliers final: 15 residues processed: 131 average time/residue: 0.1168 time to fit residues: 21.4380 Evaluate side-chains 133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 4.9990 chunk 83 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN H 92 GLN ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.099335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.067268 restraints weight = 34281.987| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.38 r_work: 0.2836 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 13288 Z= 0.210 Angle : 0.795 59.199 19192 Z= 0.488 Chirality : 0.042 0.539 2193 Planarity : 0.004 0.040 1426 Dihedral : 29.953 178.599 4085 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.31 % Allowed : 26.73 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 2.86 (0.30), residues: 806 helix: 3.09 (0.22), residues: 543 sheet: 0.72 (1.04), residues: 26 loop : -0.97 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.000 ARG K 54 TYR 0.027 0.002 TYR F 88 PHE 0.011 0.001 PHE K 4 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.21 (13288) covalent geometry : angle 0.79506 / 0.49 (19192) hydrogen bonds : bond 0.05304 / 3.56 ( 775) hydrogen bonds : angle 2.94944 / 2.06 ( 1944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8692 (tp30) cc_final: 0.8447 (tp30) REVERT: B 93 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7501 (mt0) REVERT: C 38 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7467 (p0) REVERT: C 64 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8414 (tt0) REVERT: D 39 TYR cc_start: 0.8411 (t80) cc_final: 0.8170 (t80) REVERT: E 73 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8574 (tt0) REVERT: G 95 LYS cc_start: 0.8642 (tptp) cc_final: 0.8222 (ttmm) REVERT: G 99 ARG cc_start: 0.8244 (mmt-90) cc_final: 0.7574 (mtp85) REVERT: K 1 MET cc_start: 0.6905 (ppp) cc_final: 0.6326 (ppp) outliers start: 16 outliers final: 14 residues processed: 127 average time/residue: 0.1148 time to fit residues: 20.6770 Evaluate side-chains 133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 82 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 72 optimal weight: 30.0000 chunk 92 optimal weight: 20.0000 chunk 40 optimal weight: 0.0570 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 overall best weight: 0.5700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 92 GLN ** K 2 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 = 0.3696 r_free = 0.3696 target = 0.099286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.067266 restraints weight = 34226.917| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.37 r_work: 0.2837 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 13288 Z= 0.202 Angle : 0.656 22.676 19192 Z= 0.410 Chirality : 0.041 0.376 2193 Planarity : 0.004 0.099 1426 Dihedral : 29.953 178.599 4085 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.31 % Allowed : 26.73 % Favored : 70.95 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 2.86 (0.30), residues: 806 helix: 3.09 (0.22), residues: 543 sheet: 0.72 (1.04), residues: 26 loop : -0.97 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.000 ARG K 54 TYR 0.027 0.002 TYR F 88 PHE 0.011 0.001 PHE K 4 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.20 (13288) covalent geometry : angle 0.65588 / 0.41 (19192) hydrogen bonds : bond 0.05304 / 3.56 ( 775) hydrogen bonds : angle 2.94944 / 2.06 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2691.23 seconds wall clock time: 46 minutes 47.36 seconds (2807.36 seconds total)