Starting phenix.real_space_refine on Thu Aug 6 00:52:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g6h_29769/08_2026/8g6h_29769.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g6h_29769/08_2026/8g6h_29769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g6h_29769/08_2026/8g6h_29769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g6h_29769/08_2026/8g6h_29769.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g6h_29769/08_2026/8g6h_29769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g6h_29769/08_2026/8g6h_29769.map" } resolution = 3.06 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= 0.002 sd= 0.017 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 314 5.49 5 S 13 5.16 5 C 7171 2.51 5 N 2423 2.21 5 O 3053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 12974 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 803 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MLY:plan-1': 1} Unresolved non-hydrogen planarities: 1 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: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MLY:plan-1': 1} Unresolved non-hydrogen planarities: 1 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: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3196 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "J" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3241 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} 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=0.52 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.52 Time building chain proxies: 2.93, per 1000 atoms: 0.23 Number of scatterers: 12974 At special positions: 0 Unit cell: (124.696, 95.048, 133.416, 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 314 15.00 O 3053 8.00 N 2423 7.00 C 7171 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: 1.05 Conformation dependent library (CDL) restraints added in 384.3 milliseconds 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 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 69.2% alpha, 5.1% beta 157 base pairs and 282 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.657A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.539A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.145A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.554A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.622A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.575A 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 'C' and resid 112 through 116 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 101 through 121 removed outlier: 3.789A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.623A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.510A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.083A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.590A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.584A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.569A pdb=" N MET H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.955A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.716A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.092A 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 removed outlier: 6.804A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.774A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.968A 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: 8.988A pdb=" N LEU K 67 " --> pdb=" O GLN K 2 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE K 4 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU K 69 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS K 6 " --> pdb=" O LEU K 69 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N LEU K 71 " --> pdb=" O LYS K 6 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 405 hydrogen bonds 810 hydrogen bond angles 0 basepair planarities 157 basepair parallelities 282 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2532 1.33 - 1.45: 4475 1.45 - 1.57: 6185 1.57 - 1.69: 626 1.69 - 1.81: 24 Bond restraints: 13842 Sorted by residual: 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 1.25e+01 bond pdb=" C3' DG J 23 " pdb=" C2' DG J 23 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DT J 22 " pdb=" C2' DT J 22 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT J -24 " pdb=" C2' DT J -24 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 13837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 19139 1.75 - 3.49: 876 3.49 - 5.24: 26 5.24 - 6.98: 7 6.98 - 8.73: 2 Bond angle restraints: 20050 Sorted by residual: angle pdb=" C3' DA J 26 " pdb=" O3' DA J 26 " pdb=" P DG J 27 " ideal model delta sigma weight residual 119.70 113.74 5.96 1.20e+00 6.94e-01 2.47e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.65 -2.75 6.00e-01 2.78e+00 2.09e+01 angle pdb=" N3 DT I 38 " pdb=" C4 DT I 38 " pdb=" O4 DT I 38 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" O4 DT J 9 " pdb=" C4 DT J 9 " pdb=" C5 DT J 9 " ideal model delta sigma weight residual 124.90 121.83 3.07 7.00e-01 2.04e+00 1.93e+01 angle pdb=" N3 DT J -24 " pdb=" C4 DT J -24 " pdb=" O4 DT J -24 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 ... (remaining 20045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 5957 35.81 - 71.61: 1534 71.61 - 107.42: 11 107.42 - 143.23: 3 143.23 - 179.03: 1 Dihedral angle restraints: 7506 sinusoidal: 5116 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 40.97 179.03 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC I 4 " pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " pdb=" P DC I 5 " ideal model delta sinusoidal sigma weight residual 220.00 88.60 131.40 1 3.50e+01 8.16e-04 1.30e+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 89.63 130.37 1 3.50e+01 8.16e-04 1.29e+01 ... (remaining 7503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2184 0.090 - 0.180: 105 0.180 - 0.270: 0 0.270 - 0.360: 0 0.360 - 0.450: 2 Chirality restraints: 2291 Sorted by residual: chirality pdb=" P DG J 27 " pdb=" OP1 DG J 27 " pdb=" OP2 DG J 27 " pdb=" O5' DG J 27 " both_signs ideal model delta sigma weight residual True 2.34 -2.79 -0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" P DA J 16 " pdb=" OP1 DA J 16 " pdb=" OP2 DA J 16 " pdb=" O5' DA J 16 " both_signs ideal model delta sigma weight residual True 2.34 -2.77 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" C3' DC I 4 " pdb=" C4' DC I 4 " pdb=" O3' DC I 4 " pdb=" C2' DC I 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 2288 not shown) Planarity restraints: 1450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 24 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ASP B 24 " 0.033 2.00e-02 2.50e+03 pdb=" O ASP B 24 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 25 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.025 2.00e-02 2.50e+03 1.05e-02 3.33e+00 pdb=" N9 DG I 47 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " -0.024 2.00e-02 2.50e+03 9.95e-03 2.97e+00 pdb=" N9 DG I 26 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.002 2.00e-02 2.50e+03 ... (remaining 1447 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2198 2.78 - 3.31: 10604 3.31 - 3.84: 24244 3.84 - 4.37: 29377 4.37 - 4.90: 42149 Nonbonded interactions: 108572 Sorted by model distance: nonbonded pdb=" N GLU C 91 " pdb=" OE1 GLU C 91 " model vdw 2.254 3.120 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH1 ARG A 131 " model vdw 2.263 3.120 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.274 3.040 nonbonded pdb=" O GLN K 62 " pdb=" OG SER K 65 " model vdw 2.283 3.040 nonbonded pdb=" O GLU K 16 " pdb=" NZ LYS K 29 " model vdw 2.291 3.120 ... (remaining 108567 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=0.52 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: 1.930 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.590 Find NCS groups from input model: 0.140 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 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 0.043 13842 Z= 0.508 Angle : 0.734 8.726 20050 Z= 0.646 Chirality : 0.045 0.450 2291 Planarity : 0.004 0.037 1450 Dihedral : 28.192 179.033 5962 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 18.90 % Favored : 81.10 % 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: 2.68 (0.30), residues: 800 helix: 2.65 (0.22), residues: 535 sheet: 1.95 (0.98), residues: 25 loop : -0.30 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 49 TYR 0.012 0.001 TYR F 51 PHE 0.009 0.001 PHE F 61 HIS 0.004 0.001 HIS K 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.51 (13842) covalent geometry : angle 0.73377 / 0.65 (20050) hydrogen bonds : bond 0.11614 / 7.33 ( 828) hydrogen bonds : angle 3.67302 / 2.60 ( 2046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.291 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.1567 time to fit residues: 25.8763 Evaluate side-chains 123 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN D 92 GLN ** K 41 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 = 0.3791 r_free = 0.3791 target = 0.119433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085574 restraints weight = 21499.373| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.19 r_work: 0.2894 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.0564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13842 Z= 0.155 Angle : 0.607 6.807 20050 Z= 0.359 Chirality : 0.045 0.229 2291 Planarity : 0.004 0.036 1450 Dihedral : 30.446 179.901 4342 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.03 % Allowed : 17.44 % Favored : 80.52 % 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: 2.94 (0.30), residues: 800 helix: 2.85 (0.22), residues: 543 sheet: 2.10 (1.00), residues: 25 loop : -0.32 (0.38), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.007 0.001 TYR H 39 PHE 0.009 0.001 PHE F 61 HIS 0.004 0.001 HIS K 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.15 (13842) covalent geometry : angle 0.60718 / 0.36 (20050) hydrogen bonds : bond 0.06087 / 3.94 ( 828) hydrogen bonds : angle 3.05249 / 2.13 ( 2046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: H 98 LEU cc_start: 0.9323 (mm) cc_final: 0.9086 (mm) outliers start: 14 outliers final: 7 residues processed: 130 average time/residue: 0.1402 time to fit residues: 24.4575 Evaluate side-chains 131 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 50.0000 chunk 12 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 99 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 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 = 0.3791 r_free = 0.3791 target = 0.119323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.085996 restraints weight = 21623.482| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.15 r_work: 0.2899 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.0690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13842 Z= 0.162 Angle : 0.592 6.956 20050 Z= 0.349 Chirality : 0.044 0.234 2291 Planarity : 0.004 0.037 1450 Dihedral : 30.542 179.915 4342 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.60 % Allowed : 17.44 % Favored : 80.96 % 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: 3.06 (0.30), residues: 800 helix: 2.95 (0.22), residues: 543 sheet: 2.59 (1.10), residues: 22 loop : -0.34 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.007 0.001 TYR F 51 PHE 0.009 0.001 PHE F 61 HIS 0.003 0.001 HIS K 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (13842) covalent geometry : angle 0.59206 / 0.35 (20050) hydrogen bonds : bond 0.05995 / 3.87 ( 828) hydrogen bonds : angle 2.92238 / 2.04 ( 2046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.288 Fit side-chains REVERT: B 93 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7339 (mp10) REVERT: C 64 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: C 73 ASN cc_start: 0.8173 (m-40) cc_final: 0.7942 (t0) REVERT: E 73 GLU cc_start: 0.8345 (pt0) cc_final: 0.8054 (pt0) REVERT: E 131 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.7864 (mtp180) REVERT: H 98 LEU cc_start: 0.9346 (mm) cc_final: 0.9119 (mm) outliers start: 11 outliers final: 7 residues processed: 130 average time/residue: 0.1555 time to fit residues: 26.9081 Evaluate side-chains 134 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 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 = 0.3754 r_free = 0.3754 target = 0.116991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.083256 restraints weight = 21509.669| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.14 r_work: 0.2845 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9151 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13842 Z= 0.267 Angle : 0.676 6.860 20050 Z= 0.383 Chirality : 0.049 0.249 2291 Planarity : 0.005 0.041 1450 Dihedral : 30.702 176.643 4342 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.03 % Allowed : 17.73 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.30), residues: 800 helix: 2.62 (0.22), residues: 542 sheet: 2.59 (1.11), residues: 22 loop : -0.53 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 55 TYR 0.011 0.002 TYR E 54 PHE 0.012 0.002 PHE H 67 HIS 0.005 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.27 (13842) covalent geometry : angle 0.67629 / 0.38 (20050) hydrogen bonds : bond 0.08300 / 5.44 ( 828) hydrogen bonds : angle 3.07943 / 2.16 ( 2046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.267 Fit side-chains REVERT: B 93 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: C 64 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: E 73 GLU cc_start: 0.8470 (pt0) cc_final: 0.8188 (pt0) REVERT: E 131 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8962 (mtp85) REVERT: H 98 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9156 (mm) outliers start: 14 outliers final: 8 residues processed: 134 average time/residue: 0.1438 time to fit residues: 25.5528 Evaluate side-chains 141 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 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 = 0.3779 r_free = 0.3779 target = 0.118548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084779 restraints weight = 21522.302| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.16 r_work: 0.2874 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2694 r_free = 0.2694 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: 0.2694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9121 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13842 Z= 0.148 Angle : 0.624 6.951 20050 Z= 0.360 Chirality : 0.045 0.223 2291 Planarity : 0.004 0.036 1450 Dihedral : 30.745 178.540 4342 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.74 % Allowed : 17.59 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.30), residues: 800 helix: 2.75 (0.22), residues: 542 sheet: 2.29 (1.15), residues: 23 loop : -0.40 (0.37), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 71 TYR 0.009 0.001 TYR F 51 PHE 0.010 0.001 PHE F 61 HIS 0.004 0.001 HIS K 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.15 (13842) covalent geometry : angle 0.62394 / 0.36 (20050) hydrogen bonds : bond 0.06324 / 4.11 ( 828) hydrogen bonds : angle 3.00829 / 2.11 ( 2046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.285 Fit side-chains REVERT: B 93 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7342 (mp10) REVERT: C 73 ASN cc_start: 0.8259 (m-40) cc_final: 0.7964 (t0) REVERT: G 36 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8604 (mtpp) REVERT: H 98 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9118 (mm) REVERT: K 1 MET cc_start: 0.6376 (tmm) cc_final: 0.6077 (tmm) outliers start: 12 outliers final: 8 residues processed: 131 average time/residue: 0.1403 time to fit residues: 24.4699 Evaluate side-chains 137 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 38 optimal weight: 0.9980 chunk 39 optimal weight: 0.0770 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 101 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN ** K 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 = 0.3780 r_free = 0.3780 target = 0.118613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.084825 restraints weight = 21506.074| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.17 r_work: 0.2879 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 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 (9 function evaluations) r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13842 Z= 0.171 Angle : 0.609 6.979 20050 Z= 0.352 Chirality : 0.045 0.237 2291 Planarity : 0.004 0.037 1450 Dihedral : 30.742 179.504 4342 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.18 % Allowed : 17.30 % Favored : 80.52 % 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: 2.88 (0.30), residues: 800 helix: 2.85 (0.22), residues: 542 sheet: 0.79 (1.56), residues: 13 loop : -0.26 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.008 0.001 TYR F 51 PHE 0.010 0.001 PHE F 61 HIS 0.002 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (13842) covalent geometry : angle 0.60934 / 0.35 (20050) hydrogen bonds : bond 0.06183 / 4.00 ( 828) hydrogen bonds : angle 2.91842 / 2.05 ( 2046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.332 Fit side-chains REVERT: A 131 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.7994 (mtp180) REVERT: B 93 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7354 (mp10) REVERT: C 64 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: C 73 ASN cc_start: 0.8174 (m-40) cc_final: 0.7914 (t0) REVERT: E 131 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.7923 (mtp180) REVERT: G 36 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8594 (mtpp) REVERT: G 73 ASN cc_start: 0.8261 (t0) cc_final: 0.7692 (t0) REVERT: H 98 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9108 (mm) REVERT: K 1 MET cc_start: 0.6322 (tmm) cc_final: 0.6115 (tmm) outliers start: 15 outliers final: 8 residues processed: 133 average time/residue: 0.1371 time to fit residues: 24.1160 Evaluate side-chains 140 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 74 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** K 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 = 0.3769 r_free = 0.3769 target = 0.117868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.083819 restraints weight = 21412.206| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.18 r_work: 0.2858 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 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 = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13842 Z= 0.202 Angle : 0.626 6.999 20050 Z= 0.360 Chirality : 0.046 0.242 2291 Planarity : 0.004 0.038 1450 Dihedral : 30.748 178.254 4342 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.62 % Allowed : 16.72 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.30), residues: 800 helix: 2.78 (0.22), residues: 542 sheet: 0.88 (1.58), residues: 13 loop : -0.32 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 55 TYR 0.008 0.001 TYR E 54 PHE 0.009 0.002 PHE F 61 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.20 (13842) covalent geometry : angle 0.62638 / 0.36 (20050) hydrogen bonds : bond 0.06896 / 4.49 ( 828) hydrogen bonds : angle 2.94795 / 2.07 ( 2046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.366 Fit side-chains REVERT: A 131 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8073 (mtp180) REVERT: B 93 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: C 64 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: E 131 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8909 (mtp85) REVERT: G 36 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8601 (mtpp) REVERT: G 73 ASN cc_start: 0.8285 (t0) cc_final: 0.7752 (t0) REVERT: H 98 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9137 (mm) outliers start: 18 outliers final: 11 residues processed: 132 average time/residue: 0.1591 time to fit residues: 27.9637 Evaluate side-chains 142 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 20.0000 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 103 optimal weight: 0.2980 chunk 55 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.118285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084800 restraints weight = 21438.802| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.13 r_work: 0.2876 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2697 r_free = 0.2697 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13842 Z= 0.168 Angle : 0.623 7.029 20050 Z= 0.357 Chirality : 0.045 0.239 2291 Planarity : 0.004 0.038 1450 Dihedral : 30.762 178.777 4342 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.05 % Allowed : 17.01 % Favored : 79.94 % 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: 2.83 (0.30), residues: 800 helix: 2.82 (0.22), residues: 542 sheet: 1.48 (1.59), residues: 12 loop : -0.33 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 96 TYR 0.009 0.001 TYR F 51 PHE 0.009 0.001 PHE F 61 HIS 0.002 0.001 HIS K 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (13842) covalent geometry : angle 0.62280 / 0.36 (20050) hydrogen bonds : bond 0.06472 / 4.20 ( 828) hydrogen bonds : angle 2.94956 / 2.07 ( 2046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.354 Fit side-chains REVERT: A 131 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8024 (mtp180) REVERT: B 93 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7367 (mp10) REVERT: C 64 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: E 131 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8865 (mtp85) REVERT: G 36 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8602 (mtpp) REVERT: G 73 ASN cc_start: 0.8250 (t0) cc_final: 0.7724 (t0) REVERT: H 98 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9117 (mm) outliers start: 21 outliers final: 13 residues processed: 134 average time/residue: 0.1566 time to fit residues: 27.9705 Evaluate side-chains 144 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 27 optimal weight: 0.0000 chunk 89 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 99 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.118133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.084291 restraints weight = 21576.985| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.16 r_work: 0.2870 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13842 Z= 0.193 Angle : 0.626 7.470 20050 Z= 0.358 Chirality : 0.045 0.246 2291 Planarity : 0.004 0.038 1450 Dihedral : 30.781 179.343 4342 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.47 % Allowed : 17.01 % Favored : 80.52 % 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: 800 helix: 2.79 (0.22), residues: 542 sheet: 1.41 (1.62), residues: 12 loop : -0.34 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 96 TYR 0.008 0.001 TYR F 51 PHE 0.009 0.002 PHE F 61 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (13842) covalent geometry : angle 0.62636 / 0.36 (20050) hydrogen bonds : bond 0.06540 / 4.24 ( 828) hydrogen bonds : angle 2.91997 / 2.05 ( 2046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.341 Fit side-chains REVERT: A 131 ARG cc_start: 0.9137 (OUTLIER) cc_final: 0.8044 (mtp180) REVERT: B 93 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: C 64 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: E 131 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8890 (mtp85) REVERT: G 36 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8573 (mtpp) REVERT: G 73 ASN cc_start: 0.8275 (t0) cc_final: 0.7698 (t0) REVERT: H 98 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9098 (mm) REVERT: K 1 MET cc_start: 0.6508 (tmm) cc_final: 0.5873 (tmm) outliers start: 17 outliers final: 11 residues processed: 131 average time/residue: 0.1595 time to fit residues: 27.8422 Evaluate side-chains 142 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 76 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 30.0000 chunk 5 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.118155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.084297 restraints weight = 21475.916| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.17 r_work: 0.2867 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13842 Z= 0.190 Angle : 0.625 7.051 20050 Z= 0.358 Chirality : 0.045 0.244 2291 Planarity : 0.004 0.038 1450 Dihedral : 30.781 179.336 4342 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.76 % Allowed : 16.86 % Favored : 80.38 % 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: 2.79 (0.30), residues: 800 helix: 2.80 (0.22), residues: 542 sheet: 1.44 (1.60), residues: 12 loop : -0.35 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 96 TYR 0.009 0.001 TYR F 51 PHE 0.009 0.002 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 (13842) covalent geometry : angle 0.62454 / 0.36 (20050) hydrogen bonds : bond 0.06516 / 4.23 ( 828) hydrogen bonds : angle 2.92474 / 2.06 ( 2046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1600 Ramachandran restraints generated. 800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8022 (mtp180) REVERT: B 93 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: C 64 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: E 131 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8881 (mtp85) REVERT: G 36 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8604 (mtpp) REVERT: G 73 ASN cc_start: 0.8210 (t0) cc_final: 0.7707 (t0) REVERT: H 98 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9100 (mm) REVERT: K 1 MET cc_start: 0.6549 (tmm) cc_final: 0.5929 (tmm) outliers start: 19 outliers final: 12 residues processed: 133 average time/residue: 0.1603 time to fit residues: 28.4473 Evaluate side-chains 144 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 50.0000 chunk 81 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 chunk 87 optimal weight: 30.0000 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.118517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.084667 restraints weight = 21439.043| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.16 r_work: 0.2879 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13842 Z= 0.152 Angle : 0.618 8.275 20050 Z= 0.355 Chirality : 0.044 0.240 2291 Planarity : 0.004 0.038 1450 Dihedral : 30.782 179.354 4342 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.47 % Allowed : 17.01 % Favored : 80.52 % 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: 2.86 (0.30), residues: 800 helix: 2.84 (0.22), residues: 542 sheet: 1.44 (1.60), residues: 12 loop : -0.32 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.009 0.001 TYR F 51 PHE 0.009 0.001 PHE F 61 HIS 0.003 0.001 HIS K 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.15 (13842) covalent geometry : angle 0.61775 / 0.35 (20050) hydrogen bonds : bond 0.06217 / 4.03 ( 828) hydrogen bonds : angle 2.92218 / 2.06 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3473.25 seconds wall clock time: 59 minutes 48.63 seconds (3588.63 seconds total)